This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. The Leginon software is the primary software package disseminated through the Resource. The Leginon software controls the microscope and camera system, and is responsible for a complex set of tasks normally performed by the microscope operator. The system can typically acquire many thousands of images at a variety of magnification scales over the course of a single experiment and these images and the parameters associated with them are managed by a relational database. Leginon ideally runs as a distributed system communicating over a network to the instruments, database and file storage all of which may be located on separate computers. The system requires installation of the Python programming package and extensions on all computers that will run Leginon, a MySQL database on a computer supporting the database, and a webserver with PHP on a computer that will display the images in the web based viewers. In addition the Leginon applications require careful calibrations and setup procedures in order to work efficiently and effectively. Transferring a complex system of this sort to academic labs, which might not include support from high level computer personnel, is a major challenge.